gmane.science.biology.informatics.conductor

Re: connect to HapMart with biomaRt

Steffen Durinck — 2008-05-18T02:04:47

Hi Richard, No unfortunately the status of the HapMap BioMart has not changed since. All available BioMarts are displayed by listMarts() Cheers, Steffen ----- Original Message ----- From: Richard Pearson public.gmane.org> Date: Saturday, May 17, 2008 5:40 am Subject: Re: [BioC] connect to HapMart with biomaRt To: Steffen Durinck public.gmane.org> Cc: bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

BIRD 08: Call for participants

Prof. Roland Wagner — 2008-05-17T12:51:27

Call for participants BIRD'08 2nd International Conference on Bioinformatics Research and Development www.birdconf.org Technical University of Vienna, Austria July 7-9, 2008 Best regards Roland Wagner

Re: connect to HapMart with biomaRt

Richard Pearson — 2008-05-17T12:35:22

Hi Steffen Just wondering - has there been any change on this since your post in early 2007 - i.e. do HapMap now have webservice or public MySQL capabilities? Best wishes Richard. Steffen Durinck wrote:

Re: GEOquery package

Tony Chiang — 2008-05-16T21:30:07

Hi Justin, First thing you should do is to update your R to 2.7.0 as your version is about a year out-dated. Then see if you can load the GEOquery package. Generally, you want to have the latest version of R and the packages so people who maintain the software can be more help. Usually they don't/can't help with outdated software. Cheers, --tony On Fri, May 16, 2008 at 9:58 PM, Balko, Justin M public.gmane.org> wrote: [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Re: GEOquery package

Robert Gentleman — 2008-05-16T21:27:24

Balko, Justin M wrote: Hi Justin, 2.7.0 is the current version of R, so updating it is the first thing to do. Then please tell us what version of GEOquery you tried to install (probably it is not designed for R 2.5.0, and hence your problem). best wishes Robert

GEOquery package

Balko, Justin M — 2008-05-16T20:58:56

Hello, Im running R 2.5.0 When I load the R package GEOquery, I am getting the following error: the part of the args list of 'list' being evaluated was: (header = list(), ) Error in makeClassRepresentation(Class, properties, superClasses, prototype, : element 2 is empty Error : unable to load R code in package 'GEOquery' Error: package/namespace load failed for 'GEOquery' Seems to have installed fine, or maybe not. package 'GEOquery' successfully unpacked and MD5 sums checked updating HTML package descriptions Any insight? Thanks! al({pkg <- select.list(sort(.packages(all.available = TRUE))) + if(nchar(pkg)) library(pkg, character.only=TRUE)}) the part of the args list of 'list' being evaluated was: (header = list(), ) Error in makeClassRepresentation(Class, properties, superClasses, prototype, : element 2 is empty Error : unable to load R code in package 'GEOquery' Error: package/namespace load failed for 'GEOquery' Justin Balko, PharmD Graduate Student Dept of Pharmaceutical

Re: Bug in base.profiles.nc (gcrma)?

Tony Chiang — 2008-05-16T18:09:39

Hi Heidi, It certainly looks like you found a bug. And I think this has not been fixed because I just had a peek at the source file. Can you send a note to the maintainer with your patch? That is can you download the source file via svn, change the code and then send the maintainer the output of svn diff? If you don't have svn, let me know and I can do this for you. It might also be a good idea to update your R since the stable version of R 2.7.0 was released a few weeks ago, and someone might yell at you about updating your R because there can be instances that your version of some package is outdated because your R is outdated (not true in this case). Cheers, --tony On Fri, May 16, 2008 at 6:48 PM, Heidi Dvinge public.gmane.org> wrote: [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the a

Re: question on affyQCReport vignette

Mark Kimpel — 2008-05-16T17:54:28

Thanks for reminding me about the citation function, but what I had in mind was more than just a way to cite the package itself. The package authors rely on published findings of others, as well as other packages that they depend on, and it would be nice to make sure credit is given where credit is due. Although each user could (and in the absence of other information should) track down all the papers that contribute to a package, I think it would be nice if the package maintainers include that information in the output to citation("foo"). The developers/maintainers are in the best position to know what papers they have relied on and, lets face it, there is less work for everyone if the maintainer does it once and says all his/her users the work of doing it hundreds of times for themselves. Mark On Fri, May 16, 2008 at 12:23 AM, Keith Satterley public.gmane.org> wrote:

Bug in base.profiles.nc (gcrma)?

Heidi Dvinge — 2008-05-16T17:48:31

Hi, I'm trying to use gcrma with affinity.source= "local", and a predefined set of NCprobes with gcrma v. 2.12.0. However, I'm running into problems with the sub-function base.profiles.nc. I think that where it says: if (length(seqs) < length(NCprobe)) { cat("\nNote: some of your negative control probes do not have sequence information\n") subIndex2 <- match(c(xy2indices(p$x, p$y, cdf = cdfpackagename), xy2indices(p$x, p$y + 1), cdf = cdfpackagename), NCprobe) subIndex2 <- subIndex2[!is.na(subIndex2)] bgy <- bgy[!is.na(subIndex1), ] } isn't is supposed to be: if (length(seqs) < length(NCprobe)) { cat("\nNote: some of your negative control probes do not have sequence information\n") subIndex2 <- match(c(xy2indices(p$x, p$y, cdf = cdfpackagename), xy2indices(p$x, p$y + 1, cdf = cdfpackagename)), # moving the ")" here NCprobe) subIndex2 <- subIndex2[!is.na(subIndex2)] bgy <- bgy[

Re: heatmap.2 - centering the color ramp

Artur Veloso — 2008-05-16T16:01:51

Dear Hartmut, Does breaks do what you need? heatmap.2(mdat,Rowv=NULL,Colv="Rowv", scale="none",col=greenred(75),key=TRUE, symkey=FALSE, density.info="none", trace="none",dendrogram="none" ,breaks=seq(-1,1,length.out=76)) Cheers, Artur On Fri, May 16, 2008 at 11:51 AM, Hartmut Scheel public.gmane.org> wrote: [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

heatmap.2 - centering the color ramp

Hartmut Scheel — 2008-05-16T15:51:12

Hello, a short question. How would one manage to have the color range centred around 0 instead of assigning the extreme colors (say red and green) to the lowest and largest value? Black should be at "0" and not at the mean value between the largest and the smallest value. I need to compare different heatmaps. Thanks for any suggestion Hartmut Here some simple Data: mdat <- matrix(c(1.09761079662642,0.552868871011303,0.236339539168374,-0.1568201 09742826,0.0908534304511135,-0.500217879852688,-0.182786075741673,-0.248 107861595691,-0.362157939675895),ncol=3,nrow=3,dimnames=list(c("C1","C2" ,"C3"),c("T1","T2","T3"))) heatmap.2(mdat,Rowv=NULL,Colv="Rowv", scale="none",col=greenred(75),key=TRUE, symkey=FALSE, density.info="none", trace="none",dendrogram="none") [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives:

lumiMouseV1 trouble

Davis, Wade — 2008-05-16T14:49:56

Hello BioC community: I am having trouble with lumiMouseV1. I am able to go from ID -> ENTREZID via lumiMouseV1ENTREZID: lumiMouseV1ENTREZID,ifnotfound=NA) $iSh39ilew_g4tR.A18 [1] 78928 $`GI_10304988-S` [1] NA $oS6QgIgopJKKQ4S9Ko [1] 16728 $`GI_12963686-S` [1] NA $`GI_12963764-I` [1] NA $`GI_13385605-S` [1] NA However, when I do the same for ID -> GO, every entry is NA. $iSh39ilew_g4tR.A18 [1] NA $`GI_10304988-S` [1] NA $oS6QgIgopJKKQ4S9Ko [1] NA $`GI_12963686-S` [1] NA $`GI_12963764-I` [1] NA $`GI_13385605-S` [1] NA (This is just a snippet, but they are all NA) Looking at the info for LumiMouseV1() shows Quality control information for lumiMouseV1 Date built: Created: Fri Sep 14 10:29:15 2007 Number of probes: 39562 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: lumiMouseV1ACCNUM found 39562 of 39562 lumiMouseV1CHRLOC found 27910 of 39562 lumiMouseV1CHR found 30304 of 39562 lumiMouseV1ENTREZID found

Re: gcRMA: problem compute.affinities.local on gngnf1musa

Julien Roux — 2008-05-16T14:48:36

Thanks Jim for this clear explanation. I will contact the authors of the method to get their comments on using compute.affinities() instead of compute.affinities.local() Regards, Julien James W. MacDonald a écrit :

Re: RCurl compilation error - fedora 7

martin sikora — 2008-05-16T10:10:40

robert, joern, problem solved, thanks for your quick response! it was indeed a problem with R 2.6.2 for me. i added the CRAN repository to my yum configuration (because in the official fedora ones the last R version is still 2.6.2) and upgraded to 2.7.0, now everything is fine. once again thanks for your help. cheers martin Robert Gentleman wrote: [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Re: question on affyQCReport vignette

Keith Satterley — 2008-05-16T04:23:12

Hi Mark, are you aware of the citation("package_name") command. See limma package for an example. I notice that the affyQCReport citation is auto generated. Perhaps more package authors should be encouraged to take control of what citation() reports. cheers, Keith ======================== Keith Satterley Bioinformatics Division The Walter and Eliza Hall Institute of Medical Research Parkville, Melbourne, Victoria, Australia ======================= Mark Kimpel wrote: _______________________________________________ Bioconductor mailing list Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

question on affyQCReport vignette

Mark Kimpel — 2008-05-16T00:34:47

I am a satistified user of affyQCReport and want to make sure that I include the appropriate citations in a paper I am submitting. As this package is sort of a wrapper for some other packages and the vignette does not include any references beyond that of Gautier, et al, which describes the affy package, could someone be kind enough to supply me with the appropriate citations? In general, it is sort of a pet peeve of mine that developers rightly want their work cited, but too often I feel that the citation information on the help(package == "foo") page is imcomplete. Would it be presumtuous to ask for developers to include a handy list of citations for their packages, package dependencies, etc. as part of the general help page for their package? I don't know what the official R/BioC policy is on this, but it would be extremely helpful both to users and those whose original ideas are incorporated into R/BioC. And, if I"ve missed something obvious, point me in the right direction, spank me with a wet noodle

Re: converting gene name to affy probe

Ruppert Valentino — 2008-05-15T22:27:42

Hi Jim, thanks for the advise the problem here is I have a list of genes and if I use mget instead of get then it give me a list so what i like to do is to convert list of genes to their probes but based on what you mentioned its not hard to get it to work. thanks Ruppert> Date: Thu, 15 May 2008 10:06:03 -0400> From: jmacdon-mMBBrLdnlFaUArH+D2fLrA< at >public.gmane.org> To: ruppert7-PkbjNfxxIARBDgjK7y7TUQ< at >public.gmane.org> CC: bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org> Subject: Re: [BioC] converting gene name to affy probe> > Actually, that isn't what you want. That's like driving a nail with the > butt-end of a screwdriver. It will eventually do what you want, but that > hammer sitting there is much more efficient. ;-D> > > get("VEGFA", revmap(hgu133aSYMBOL))> [1] "210512_s_at" "210513_s_at" "211527_x_at" "212171_x_at"> > And to get the symbol, given the probe ID> > > get("210512_s_at", hgu133aSYMBOL)> [1] "VEGFA"> > or if the symbol you have is not found:> > > get("DKFZp779B086", rev

Re: GSEABase how to map gene symbols to mouse EntrezId or Affy

Martin Morgan — 2008-05-15T18:47:40

Always use accessors, geneIds(gss[[1]]), ... be nice to your helpers with complete examples, I guess capwords is then More on this below... mapIdentifiers provides a convenient side door in the form of Function: mapIdentifiers (package GSEABase) what="GeneColorSet", to="GeneIdentifierType", from="environment" what="GeneSet", to="GeneIdentifierType", from="environment" which is to say that if you have a custom mapping you can represent it as an environment with keys equal to the identifiers you're mapping from and values the identifiers you're mapping to, e.g., probably you want to inject information about the identifiers you are mapping to, e.g., that they are mouse, using as the second argument EntrezIdentifier('org.Mm.eg.db') There doesn't seem to be a method defined for gene set collections (an oversight), but you can back to... There are a bunch of ways through this, but I would avoid using direct slot access. One possibility would be Martin

Re: help about ReadAffy() erro

James W. MacDonald — 2008-05-15T13:32:14

Hi Melody, First off, note that a simple search for 'cannot allocate vector' using the Gmane search functions on the BioC website would have come up with probably hundreds of hits that would have answered this question for you. xiong mody0911 wrote: Not sure what you are asking here, but there are three things you can do. First, try justRMA() or justGCRMA(). Second, use RMAexpress (Google it). Third, buy RAM. Best, Jim

Re: gcRMA: problem compute.affinities.local on gngnf1musa

James W. MacDonald — 2008-05-15T13:25:52

Hi Julien, Julien Roux wrote: From the source for these functions: ##this is almost the same as compute.affinities ##except that affinity.spline.coefs is not loaded with data() ##but computed using the data provided by the user So I have to assume that the probe package for your chip has some probes in which Affy used the 'N' IUPAC symbol. Since gcrma doesn't understand anything but ACTG, this causes the error. So when you use compute.affinities(), you load the pre-calculated affinity data rather than using the sequences from your chip. Hence no error. Best, Jim

Re: GSEABase how to map gene symbols to mouse EntrezId orAffy

Vladimir Morozov — 2008-05-15T17:56:26

Martin, You are right that disagreement beween human and mouse symblos is the problem. But you still should get some mapping if translate symbols into capwords [1] 0 sum(!is.na(mget(capwords(tolower(gss[[1]]< at >geneIds)),org.Mm.egSYMBOL2EG,i fnotfound=NA))) [1] 46 Let's say I will figure out some mapping using ortholog or alias names. Will I screw the GeneSet data structure by gss2 <- lapply(gss,function(x){x< at >geneIds <- my.mapping(x< at >geneIds);x< at >geneIdType< at >type <- 'EntrezIdentifier'}) ? Vladimir Morozov -----Original Message----- From: Martin Morgan [mailto:mtmorgan-q9hIisBwmLrYtjvyW6yDsg< at >public.gmane.org] Sent: Thursday, May 15, 2008 12:56 PM To: Vladimir Morozov Cc: bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7< at >public.gmane.org Subject: Re: [BioC] GSEABase how to map gene symbols to mouse EntrezId or Affy Hi Vladimir -- "Vladimir Morozov" public.gmane.org> writes: mapIdentifiers needs to know where to look for the map. I guess the way you created gss means that it doesn't know